A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

Nucleic Acids Research

Volumn 35, Issue 12, 2007, Pages 4195-4202

  Sturm, Marc ^a   Quinten, Sascha ^b   Huber, Christian G ^b   Kohlbacher, Oliver ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ARTICLE; CALCULATION; ION PAIR CHROMATOGRAPHY; LOW TEMPERATURE; MODEL; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; STATISTICAL ANALYSIS; SUPPORT VECTOR MACHINE; ARTIFICIAL INTELLIGENCE; CHEMISTRY; CONFORMATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ISOLATION AND PURIFICATION; METHODOLOGY; REPRODUCIBILITY; SEQUENCE HOMOLOGY; STATISTICAL MODEL; TEMPERATURE; VALIDATION STUDY;

ARTIFICIAL INTELLIGENCE; BASE SEQUENCE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; MODELS, STATISTICAL; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; REPRODUCIBILITY OF RESULTS; SEQUENCE HOMOLOGY, NUCLEIC ACID; TEMPERATURE;

EID: 34547641914     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm338     Document Type: Article

References (16)

1. Gelhaus,S., LaCourse,W.R., Hagan,N.A., Amarasinghe,G.K. and Fabris,D. (2003) Rapid purification of RNA secondary structures. Nucleic Acids Res., 31, e135.
2. Huber,C.G. and Berti,G.N. (1996) Detection of partial denaturation in AT-rich DNA fragments by ion-pair reversed-phase chromatography. Anal. Chem., 68, 2959-2965.
3. Braun,A., Little,D.P. and Koster,H. (1997) Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry. Clin. Chem., 43, 1151-1158.
4. Sanger,F., Nicklen,S. and Coulson,A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5467.
5. Bumcrot,D., Manoharan,M., Koteliansky,V. and Sah,D.W.Y. (2006) RNAi therapeutics: A potential new class of pharmaceutical drugs. Nat. Chem. Biol., 2, 711-719.
6. Tan,L.C., Carr,P.W. and Abraham,M.H. (1996) Study of Retention in reversed-phase liquid chromatography using linear solvation energy relationships I. The Stationary Phase. J. Chromatogr. A, 752 1-18.
7. Gilar,M., Fountain,K.J., Budman,Y., Neue,U.D., Yardley,K.R., Rainville,P.D., Russell,R.J. and Gebler,J.C. (2002) Ion-pair reversed-phase high-performance liquid chromatography analysis of oligonucleotides: Retention prediction. J. Chromatogr. A, 958 167-82.
8. Hoffmann,R., Bril,G., Yoneyama,M. and Otvos,L. (1998) Prediction of retention times of peptide nucleic acids during reversed-phase high-performance liquid chromatography. J. Chromatogr. A, 814 111-119.
9. Meek,J.L. (1980) Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition. Proc. Natl Acad. Sci. USA, 77, 1632-1636.
10. Guo,D., Mant,C.T., Taneja,A.K., Parker,J.M.R. and Hodges,R.S. (1986) Prediction of peptide retention times in reversed phase HPLC: determination of retention coefficients of amino acid residues of model synthetic peptides. J. Chromatogr., 359, 499-518.
11. Huber,C.G., Premstaller,A. and Oberacher,H. (2001) Method and apparatus for separating polynucleotides using monolithic capillary columns. Patent application U.S., 09/770410.
12. Vapnik,V.N. (2001) The Nature of Statistical Learning Theory. Springer-Verlag New York Inc., New York, USA.
13. Schölkopf,B., Smola,A.J., Williamson,R.C. and Bartlett,P.L. (2000) New support vector algorithms. Neural Computation, 12, 1207-1245.
14. Hofacker,I.L., Fontana,W., Stadler,P.F., Bonhoeffer,L.S., Tacker,M. and Schuster,P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188.
15. Rice,P., Longden,I. and Bleasby,A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
16. Sugimoto,N., Nakano,S., Yoneyama,M. and Honda,K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res., 24, 4501-4505.